Three-dimensional MHD equilibria including the bootstrap current self-consistently are studied for the Large Helical Device (LHD). The magnitude of the bootstrap current is sensitive to the magnetic axis position or the Shafranov shift in LHD, which is proportional to the plasma pressure and inversely proportional to the rotational transform. Since the bootstrap current enhances the rotational transform and reduces the Shafranov shift, the self-consistent MHD equilibrium is crucial for estimating the bootstrap current. The total bootstrap current exceeds 100 kA for LHD plasmas with volume averaged beta ⟨β⟩ ≳ 1% if both electrons and ions belong to the almost collisionless 1/ν regime in the whole plasma region. Effects of the vertical field, the quadrupole field and the pressure profile on the bootstrap current are also investigated